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<li class="navelem"><a class="el" href="namespaceOpenMS.html">OpenMS</a></li><li class="navelem"><a class="el" href="classOpenMS_1_1PeakIntensityPredictor.html">PeakIntensityPredictor</a></li> </ul>
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<a href="#pub-methods">Public Member Functions</a> |
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<p>Predict peak heights of peptides based on Local Linear Map model.
<a href="classOpenMS_1_1PeakIntensityPredictor.html#details">More...</a></p>
<p><code>#include <<a class="el" href="PeakIntensityPredictor_8h_source.html">OpenMS/ANALYSIS/PIP/PeakIntensityPredictor.h</a>></code></p>
<table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-methods"></a>
Public Member Functions</h2></td></tr>
<tr class="memitem:a642d8d6e934571ab08e42d42781fdd33"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1PeakIntensityPredictor.html#a642d8d6e934571ab08e42d42781fdd33">predict</a> (const <a class="el" href="classOpenMS_1_1AASequence.html">AASequence</a> &sequence)</td></tr>
<tr class="memdesc:a642d8d6e934571ab08e42d42781fdd33"><td class="mdescLeft"> </td><td class="mdescRight">Returns predicted peak heights (intensites) of a single peptide. <a href="#a642d8d6e934571ab08e42d42781fdd33">More...</a><br/></td></tr>
<tr class="separator:a642d8d6e934571ab08e42d42781fdd33"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a314932ca8882fe700bff601e89e90f97"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1PeakIntensityPredictor.html#a314932ca8882fe700bff601e89e90f97">predict</a> (const <a class="el" href="classOpenMS_1_1AASequence.html">AASequence</a> &sequence, std::vector< <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> > &add_info)</td></tr>
<tr class="memdesc:a314932ca8882fe700bff601e89e90f97"><td class="mdescLeft"> </td><td class="mdescRight">Returns predicted peak heights (intensites) of a single peptide. <a href="#a314932ca8882fe700bff601e89e90f97">More...</a><br/></td></tr>
<tr class="separator:a314932ca8882fe700bff601e89e90f97"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:aa762089eb35938ea2d0c41f22864919f"><td class="memItemLeft" align="right" valign="top">std::vector< <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> > </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1PeakIntensityPredictor.html#aa762089eb35938ea2d0c41f22864919f">predict</a> (const std::vector< <a class="el" href="classOpenMS_1_1AASequence.html">AASequence</a> > &sequences)</td></tr>
<tr class="memdesc:aa762089eb35938ea2d0c41f22864919f"><td class="mdescLeft"> </td><td class="mdescRight">Returns predicted peak heights (intensites) of several peptides. <a href="#aa762089eb35938ea2d0c41f22864919f">More...</a><br/></td></tr>
<tr class="separator:aa762089eb35938ea2d0c41f22864919f"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a8fbba4fce219eac2e4849d7325a7a0fd"><td class="memItemLeft" align="right" valign="top">std::vector< <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> > </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1PeakIntensityPredictor.html#a8fbba4fce219eac2e4849d7325a7a0fd">predict</a> (const std::vector< <a class="el" href="classOpenMS_1_1AASequence.html">AASequence</a> > &sequences, std::vector< std::vector< <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> > > &add_info)</td></tr>
<tr class="memdesc:a8fbba4fce219eac2e4849d7325a7a0fd"><td class="mdescLeft"> </td><td class="mdescRight">Returns predicted peak heights (intensites) of several peptides. <a href="#a8fbba4fce219eac2e4849d7325a7a0fd">More...</a><br/></td></tr>
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<tr><td colspan="2"><div class="groupHeader"></div></td></tr>
<tr class="memitem:a9dffd5d331794041c30ee8179a71a09c"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1PeakIntensityPredictor.html#a9dffd5d331794041c30ee8179a71a09c">PeakIntensityPredictor</a> ()</td></tr>
<tr class="memdesc:a9dffd5d331794041c30ee8179a71a09c"><td class="mdescLeft"> </td><td class="mdescRight">Constructors and Destructors. <a href="#a9dffd5d331794041c30ee8179a71a09c">More...</a><br/></td></tr>
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<tr class="memitem:ae677bc2f893383c3ef8d246731137baf"><td class="memItemLeft" align="right" valign="top">virtual </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1PeakIntensityPredictor.html#ae677bc2f893383c3ef8d246731137baf">~PeakIntensityPredictor</a> ()</td></tr>
<tr class="memdesc:ae677bc2f893383c3ef8d246731137baf"><td class="mdescLeft"> </td><td class="mdescRight">destructor <a href="#ae677bc2f893383c3ef8d246731137baf">More...</a><br/></td></tr>
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<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pri-methods"></a>
Private Member Functions</h2></td></tr>
<tr class="memitem:a9abb92b2cf4a88dc21e0e4c8003cc882"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1PeakIntensityPredictor.html#a9abb92b2cf4a88dc21e0e4c8003cc882">map_</a> (const std::vector< <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> > &data)</td></tr>
<tr class="memdesc:a9abb92b2cf4a88dc21e0e4c8003cc882"><td class="mdescLeft"> </td><td class="mdescRight">calculate and return predicted value based on given <a class="el" href="classOpenMS_1_1LocalLinearMap.html" title="Trained Local Linear Map (LLM) model for peak intensity prediction. ">LocalLinearMap</a> model for corresponding aaindex variables <a href="#a9abb92b2cf4a88dc21e0e4c8003cc882">More...</a><br/></td></tr>
<tr class="separator:a9abb92b2cf4a88dc21e0e4c8003cc882"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a629f78c731e498f714bf6b6795cff871"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1PeakIntensityPredictor.html#a629f78c731e498f714bf6b6795cff871">findWinner_</a> (const std::vector< <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> > &data)</td></tr>
<tr class="memdesc:a629f78c731e498f714bf6b6795cff871"><td class="mdescLeft"> </td><td class="mdescRight">find winning prototype <a href="#a629f78c731e498f714bf6b6795cff871">More...</a><br/></td></tr>
<tr class="separator:a629f78c731e498f714bf6b6795cff871"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a9ffa9b685036c2da0261a8d3dbbf3ae9"><td class="memItemLeft" align="right" valign="top">std::vector< <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> > </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1PeakIntensityPredictor.html#a9ffa9b685036c2da0261a8d3dbbf3ae9">calculateAddInfo_</a> (const std::vector< <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> > &data)</td></tr>
<tr class="memdesc:a9ffa9b685036c2da0261a8d3dbbf3ae9"><td class="mdescLeft"> </td><td class="mdescRight">calculate assignments of peptides to cluster and the corresponding error <a href="#a9ffa9b685036c2da0261a8d3dbbf3ae9">More...</a><br/></td></tr>
<tr class="separator:a9ffa9b685036c2da0261a8d3dbbf3ae9"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a074dc4aa56c79daa8a1743f7c900e366"><td class="memItemLeft" align="right" valign="top">std::vector< <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> > </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1PeakIntensityPredictor.html#a074dc4aa56c79daa8a1743f7c900e366">getPropertyVector_</a> (const <a class="el" href="classOpenMS_1_1AASequence.html">AASequence</a> &sequence)</td></tr>
<tr class="memdesc:a074dc4aa56c79daa8a1743f7c900e366"><td class="mdescLeft"> </td><td class="mdescRight">Calculates an array of properties for an amino acid sequence. <a href="#a074dc4aa56c79daa8a1743f7c900e366">More...</a><br/></td></tr>
<tr class="separator:a074dc4aa56c79daa8a1743f7c900e366"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a4368de771b0baee8923b88519ce1e567"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1PeakIntensityPredictor.html#a4368de771b0baee8923b88519ce1e567">PeakIntensityPredictor</a> (const <a class="el" href="classOpenMS_1_1PeakIntensityPredictor.html">PeakIntensityPredictor</a> &llmModel)</td></tr>
<tr class="memdesc:a4368de771b0baee8923b88519ce1e567"><td class="mdescLeft"> </td><td class="mdescRight">copy constructor not impemented => private <a href="#a4368de771b0baee8923b88519ce1e567">More...</a><br/></td></tr>
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<tr class="memitem:af200fbf58f9d7943ba40f03439fbd697"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1PeakIntensityPredictor.html">PeakIntensityPredictor</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1PeakIntensityPredictor.html#af200fbf58f9d7943ba40f03439fbd697">operator=</a> (const <a class="el" href="classOpenMS_1_1PeakIntensityPredictor.html">PeakIntensityPredictor</a> &peakIntensityPredictor)</td></tr>
<tr class="memdesc:af200fbf58f9d7943ba40f03439fbd697"><td class="mdescLeft"> </td><td class="mdescRight">assignment operator not impemented => private <a href="#af200fbf58f9d7943ba40f03439fbd697">More...</a><br/></td></tr>
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Private Attributes</h2></td></tr>
<tr class="memitem:a18e98144069006e122c8b1acbb0c5006"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1LocalLinearMap.html">LocalLinearMap</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1PeakIntensityPredictor.html#a18e98144069006e122c8b1acbb0c5006">llm_</a></td></tr>
<tr class="memdesc:a18e98144069006e122c8b1acbb0c5006"><td class="mdescLeft"> </td><td class="mdescRight">Local Linear Map model. <a href="#a18e98144069006e122c8b1acbb0c5006">More...</a><br/></td></tr>
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<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
<div class="textblock"><p>Predict peak heights of peptides based on Local Linear Map model. </p>
<p>This class can be used for predictions of peptide peak heights (referred to as intensities) from a peptide sequence by a Local Linear Map (LLM) model. A general introduction to the Peak Intensity Predictor (PIP) can be found in the <a href="tutorial_pip.html">PIP Tutorial</a>.</p>
<p>The predictor performs only on the peptides sequences as an <a class="el" href="classOpenMS_1_1AASequence.html" title="Representation of a peptide/protein sequence. ">AASequence</a> representation. Every sequence is transformed to an 18 dimensional data vector representing certain chemical characteristics and is loaded into the trained <a class="el" href="classOpenMS_1_1LocalLinearMap.html" title="Trained Local Linear Map (LLM) model for peak intensity prediction. ">LocalLinearMap</a> model to find the predicted peptides peak intensity.</p>
<p>Every predictor object calls the appropriate LocalLinearMap model, transforms the given sequences and creates a vector space in which the LocalLinearMap performs. </p>
</div><h2 class="groupheader">Constructor & Destructor Documentation</h2>
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<p>Constructors and Destructors. </p>
<p>default constructor </p>
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<td class="memname">virtual ~<a class="el" href="classOpenMS_1_1PeakIntensityPredictor.html">PeakIntensityPredictor</a> </td>
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<p>destructor </p>
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<h2 class="groupheader">Member Function Documentation</h2>
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<td class="memname">std::vector<<a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a>> calculateAddInfo_ </td>
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<p>calculate assignments of peptides to cluster and the corresponding error </p>
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<td class="memname"><a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> findWinner_ </td>
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<p>find winning prototype </p>
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<td class="memname">std::vector<<a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a>> getPropertyVector_ </td>
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<p>Calculates an array of properties for an amino acid sequence. </p>
<p>The array contains the following properties:</p>
<ul>
<li>0: Number of 'R' residues</li>
<li>1: Signal sequence helical potential</li>
<li>2: Number of 'F' residues</li>
<li>3: Positive charge</li>
<li>4: Helix-coil equilibrium constant</li>
<li>5: Estimated gas-phase basicity at 500 K</li>
<li>6: Number of 'H' residues</li>
<li>7: Kerr-constant increments</li>
<li>8: Number of 'M' residues</li>
<li>9: Average amino acid weight</li>
<li>10: Hydropathy scale (36% accessibility)</li>
<li>11: Hydropathy scale (50% accessibility)</li>
<li>12: Optimized average non-bonded energy per atom</li>
<li>13: Number of 'Q' residues</li>
<li>14: Information measure for extended without H-bond</li>
<li>15: Relative population of conformational state E</li>
<li>16: Hydrophobicity coefficient in RP-HPLC, C8 with 0.1TFA/MeCN/H2 O,</li>
<li>17: Number of 'Y' residues</li>
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<td class="memname"><a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> map_ </td>
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<p>calculate and return predicted value based on given <a class="el" href="classOpenMS_1_1LocalLinearMap.html" title="Trained Local Linear Map (LLM) model for peak intensity prediction. ">LocalLinearMap</a> model for corresponding aaindex variables </p>
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<td class="memname"><a class="el" href="classOpenMS_1_1PeakIntensityPredictor.html">PeakIntensityPredictor</a>& operator= </td>
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<p>assignment operator not impemented => private </p>
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<td class="memname"><a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> predict </td>
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<p>Returns predicted peak heights (intensites) of a single peptide. </p>
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<p>Returns predicted peak heights (intensites) of a single peptide. </p>
<p>Some additional information is returned in <code>add_info</code> :</p>
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<li>0: x coordinates of associated cluster (first column)</li>
<li>1: y coordinates of associated cluster (2nd column)</li>
<li>2: error (RMSE) of the peptide to the associated next prototype (cluster center) </li>
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<p>Returns predicted peak heights (intensites) of several peptides. </p>
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<p>Returns predicted peak heights (intensites) of several peptides. </p>
<p>Some additional information foreach peptide is returned in <code>add_info</code> . For each peptide a row with the following components is returned:</p>
<ul>
<li>0: x coordinates of associated cluster (first column)</li>
<li>1: y coordinates of associated cluster (2nd column)</li>
<li>2: error (RMSE) of the peptide to the associated next prototype (cluster center) </li>
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<h2 class="groupheader">Member Data Documentation</h2>
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<td class="memname"><a class="el" href="classOpenMS_1_1LocalLinearMap.html">LocalLinearMap</a> llm_</td>
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<p>Local Linear Map model. </p>
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<TD><font color="#c0c0c0">OpenMS / TOPP release 1.11.1</font></TD>
<TD align="right"><font color="#c0c0c0">Documentation generated on Thu Nov 14 2013 11:19:27 using doxygen 1.8.5</font></TD>
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